ZAP70

protein-coding

zeta chain of T cell receptor associated protein kinase 70, the group of Syk family tyrosine kinases|SH2 domain containing

Gene summary

This gene encodes an enzyme belonging to the protein tyrosine kinase family, and it plays a role in T-cell development and lymphocyte activation. This enzyme, which is phosphorylated on tyrosine residues upon T-cell antigen receptor (TCR) stimulation, functions in the initial step of TCR-mediated signal transduction in combination with the Src family kinases, Lck and Fyn. This enzyme is also essential for thymocyte development. Mutations in this gene cause selective T-cell defect, a severe combined immunodeficiency disease characterized by a selective absence of CD8-positive T-cells. Two transcript variants that encode different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

Previous symbols:
  • SRK

MANE transcript

NM_001079.4

Inheritance

AR

ClinVar variants

P:43U:198B:197

Top phenotype

Autoimmune disease, multisystem, infantile-onset 2; Immunodeficiency 48

gnomAD constraint

pLI —, LoF o/e 0.17

Max pathogenic AF

—

Genomic locus

chr2:97,713,576-97,744,327

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~30.8 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

autoimmune disease, multisystem, infantile-onset, 2STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014861

Submitter: PanelApp Australia

combined immunodeficiency due to ZAP70 deficiencySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0010023

Submitter: Labcorp Genetics (formerly Invitae)

combined immunodeficiency due to ZAP70 deficiencyDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0010023

Submitter: ClinGen

ZAP70 was first reported in relation to autosomal recessive combined immunodeficiency in 1994 (Arpaia E, et al., 1994, PMID: 8124727). ZAP70 related combined immunodeficiency is caused by abnormal T-cell receptor signaling with low to absent CD8+ T cells and normal CD3+ and CD4+ T cells numbers. Symptoms include recurrent infections, including severe lower respiratory infections and oral candidiasis, chronic diarrhea, and failure to thrive. Combined immunodeficiencies such as ZAP-70 deficiency or major histocompatibility complex (MHC) class I and II gene expression deficiency may not be detected with the TREC assay as T-cell development is intact beyond the point of T-cell receptor (TCR) gene recombination (PMID: 32579701). Six variants (missense, nonsense, frameshift, and splicing substitutions) that have been reported in six probands in six publications (PMIDs: 8124727, 28124082, 21094993, 30778343, 8202713, 8202712) are included in this curation. Variants in this gene segregated with disease in two additional family members (PMIDs: 27448562). Heterozygous carriers in these families did not show evidence of pathogenicity.The mechanism of pathogenicity is known to be loss of function. This gene-disease association is also supported by animal models, expression studies, biochemical studies, and functional studies in patient cells (PMIDs: 27869819, 8176201, 25092893, 25092893, 8124727). ZAP70 is expressed exclusively in T and NK cell lines and is expressed in all murine and human thymocyte subpopulations (PMID: 8176201). ZAP70 null mice have no detectable ZAP70 expression and absent T cells and when null mice with a tetracycline inducible Zap70 transgene are induced with Zap70 protein, thymocyte generation is partially restored (PMID: 25092893). ZAP70 interacts with the T cell receptor complex via its SH2 domains and is activated by Lck (PMID: 27869819). In summary, ZAP70 is definitively associated with autosomal recessive combined immunodeficiency. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This classification was approved by the ClinGen SCID/CID GCEP on January 20, 2022 (SOP Version 8).

combined immunodeficiency due to ZAP70 deficiencySUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0010023

Submitter: Orphanet

combined immunodeficiency due to ZAP70 deficiencySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0010023

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Autoimmune disease, multisystem, infantile-onset 2; Immunodeficiency 48AR

Manifestation: Allergy/Immunology/Infectious

Intervention: Allergy/Immunology/Infectious

Rationale: In Autoimmune disease, multisystem, infantile-onset 2, individuals may demonstrate multiple autoimmune sequelae that may be refractory to immunosuppressants, and HSCT has been described as effective; In Selective T-cell defect, prophylactic measures, in the short term, include IVIG administration as well as antiinfectious prophylaxis; If blood products are necessary, they should be irradiated and CMV and EBV-negative; Live vaccines should be avoided, and immunizations should be deferred until reconstitution of the immune system; HSCT has been described as effective in some individuals

Refs: 2511270; 8124727; 8202713; 8202712; 10574909; 10748099; 11123350; 11412303; 11463783; 18509675; 19548248; 20301777; 23124046; 26783323Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZAP70 variants in ClinVar

8 Conditions Cataloged
Combined immunodeficiency due to ZAP70 deficiencyTotal: 476
not providedTotal: 81
not specifiedTotal: 73
Inborn genetic diseasesTotal: 62
ZAP70-related disorderTotal: 19
Autoimmune disease, multisystem, infantile-onset, 2Total: 13
Severe combined immunodeficiency diseaseTotal: 6
Combined immunodeficiencyTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001079.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
3
clinvar
188
clinvar
1
clinvar
193
missense
2
clinvar
11
clinvar
192
clinvar
7
clinvar
1
clinvar
213
nonsense
9
clinvar
2
clinvar
2
clinvar
13
start loss
1
clinvar
1
frameshift
11
clinvar
1
clinvar
12
splice donor/acceptor (+/-2bp)
1
clinvar
5
clinvar
6
Total23201981952438

Highest pathogenic variant AF is 0.00002726501

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001079.4RefSeqNP_001070.212MANE Select
ENST00000264972.10EnsemblENSP00000264972.512MANE Select
NM_001378594.1RefSeqNP_001365523.112Standard
NM_207519.2RefSeqNP_997402.16Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
zap70Danio rerio

Structure: pro-T cell

Quality: decreased amount

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Primary immunodeficiency - Homo sapiens (human)
  • T cell receptor signaling pathway - Homo sapiens (human)
  • Th17 cell differentiation - Homo sapiens (human)
  • Th1 and Th2 cell differentiation - Homo sapiens (human)
  • Ras signaling pathway - Homo sapiens (human)

Biological Process

  • adaptive immune response
  • protein phosphorylation
  • immune response
  • peptidyl-tyrosine phosphorylation
  • T cell differentiation

Molecular Function

  • phosphotyrosine residue binding
  • protein tyrosine kinase activity
  • non-membrane spanning protein tyrosine kinase activity
  • protein binding
  • ATP binding

Cellular Component

  • immunological synapse
  • cytoplasm
  • cytosol
  • plasma membrane
  • cell-cell junction

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000264972
Coding exons
12
Length
26303
Individuals with no LoFs
125730
Homozygous LoFs
0
Heterozygous LoFs
14
Defined
125744
p
0.0000557
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.762574150.6190.00003004010
Missense (PolyPhen)97190.40.509451794
Synonymous1.091681870.8990.00001561186
Loss of Function4.11528.80.1730.00000141329

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American0.0000580.000058rare
Ashkenazi Jewish0.000200.00020rare
East Asian0.0000540.000054rare
Finnish00.0absent
European (Non-Finnish)0.0000560.000053rare
South Asian0.0000670.000065rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Tyrosine kinase that plays an essential role in regulation of the adaptive immune response. Regulates motility, adhesion and cytokine expression of mature T-cells, as well as thymocyte development. Contributes also to the development and activation of primary B-lymphocytes. When antigen presenting cells (APC) activate T-cell receptor (TCR), a serie of phosphorylations lead to the recruitment of ZAP70 to the doubly phosphorylated TCR component CD247/CD3Z through ITAM motif at the plasma membrane. This recruitment serves to localization to the stimulated TCR and to relieve its autoinhibited conformation. Release of ZAP70 active conformation is further stabilized by phosphorylation mediated by LCK. Subsequently, ZAP70 phosphorylates at least 2 essential adapter proteins: LAT and LCP2. In turn, a large number of signaling molecules are recruited and ultimately lead to lymphokine production, T-cell proliferation and differentiation. Furthermore, ZAP70 controls cytoskeleton modifications, adhesion and mobility of T-lymphocytes, thus ensuring correct delivery of effectors to the APC. ZAP70 is also required for TCR-CD247/CD3Z internalization and degradation through interaction with the E3 ubiquitin-protein ligase CBL and adapter proteins SLA and SLA2. Thus, ZAP70 regulates both T-cell activation switch on and switch off by modulating TCR expression at the T-cell surface. During thymocyte development, ZAP70 promotes survival and cell-cycle progression of developing thymocytes before positive selection (when cells are still CD4/CD8 double negative). Additionally, ZAP70-dependent signaling pathway may also contribute to primary B-cells formation and activation through B-cell receptor (BCR). {ECO:0000269|PubMed:11353765, ECO:0000269|PubMed:12051764, ECO:0000269|PubMed:1423621, ECO:0000269|PubMed:20135127, ECO:0000269|PubMed:26903241, ECO:0000269|PubMed:8124727, ECO:0000269|PubMed:8702662, ECO:0000269|PubMed:9489702}.;
Disease
DISEASE: Immunodeficiency 48 (IMD48) [MIM:269840]: A form of severe immunodeficiency characterized by a selective absence of CD8+ T-cells. {ECO:0000269|PubMed:11123350, ECO:0000269|PubMed:11412303, ECO:0000269|PubMed:18509675, ECO:0000269|PubMed:8124727, ECO:0000269|PubMed:8202713}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Autoimmune disease, multisystem, infantile-onset, 2 (ADMIO2) [MIM:617006]: An autosomal recessive, autoimmune disorder characterized by systemic manifestations including blistering skin disease, uncontrollable bullous pemphigoid, inflammatory colitis, autoimmune hypothyroidism, proteinuria and nephrotic syndrome. {ECO:0000269|PubMed:26783323}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.629

Intolerance Scores

LoFtool
0.0533
RVIS EVS
-1.16
RVIS percentile EVS
6.17

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.858

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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